Metastasis and invasion, the important characteristics of malignant tumors, are closely associated with a series of changes in the expression of genes and proteins. In this study, we compare mRNA and protein expression in high and low metastasis adenoid cystic carcinoma cell lines by mRNA suppression subtractive hybridization and two-dimensional electrophoresis combined with peptide mass fingerprint analysis. 34 differentially expressed genes were obtained using suppression subtractive hybridization experiments including 6 highly expressed gene sequences in the high metastasis cell line, and 28 in the low metastasis cell line. RNA dot blot hybridization further confirmed the results after excluding false positives. For protein analysis, ten significantly different protein spots were detected using two-dimensional gel electrophoresis technique combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI- TOF-MS). The results then compare with the SWISS PROT database. These results suggest that high tumor metastasis of adenoid cystic carcinoma is associated with multiple genes whose function include angiogenesis, protein synthesis, signal transduction, modulation of cell cycle, molecular chaperones, and immune co-stimulating molecule. Moreover, the results of the phenotypic function-related expression mapping analysis at the mRNA and protein level revealed obvious complementarities, providing important clues for further study of the molecular mechanism of metastasis, metastasis control and possible targets for cancer gene therapy. © 2004 Kluwer Academic Publishers.